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Magnesium in PDB 5a94: Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1

Enzymatic activity of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1

All present enzymatic activity of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1:
3.2.1.73;

Protein crystallography data

The structure of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1, PDB code: 5a94 was solved by G.Sulzenbacher, M.Lafond, T.Freyd, B.Henrissat, R.M.Coutinho, J.G.Berrin, M.L.Garron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.42 / 1.99
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 188.643, 132.753, 131.352, 90.00, 133.78, 90.00
R / Rfree (%) 17.9 / 19

Other elements in 5a94:

The structure of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 (pdb code 5a94). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1, PDB code: 5a94:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5a94

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Magnesium binding site 1 out of 6 in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:24.6
occ:1.00
 O A:HOH2162 2.2 23.6 1.0
O A:VAL178 2.2 21.6 1.0
O A:VAL181 2.2 20.0 1.0
O A:HOH2158 2.4 21.9 1.0
O A:HOH2159 2.5 25.9 1.0
C A:VAL178 3.3 22.6 1.0
C A:VAL181 3.3 19.9 1.0
CB A:VAL181 3.9 20.2 1.0
CA A:VAL181 4.0 20.3 1.0
N A:VAL178 4.0 22.9 1.0
CA A:VAL178 4.1 22.4 1.0
N A:VAL181 4.1 20.1 1.0
O A:TYR175 4.2 18.5 1.0
CG1 A:VAL223 4.2 24.4 1.0
N A:PRO179 4.3 22.8 1.0
CA A:PRO179 4.3 21.5 1.0
N A:ALA182 4.4 19.8 1.0
CB A:VAL178 4.4 21.3 1.0
C A:PRO179 4.5 20.9 1.0
O A:PRO179 4.5 20.9 1.0
CE1 A:PHE50 4.6 23.9 1.0
CG1 A:VAL181 4.6 20.1 1.0
OG1 A:THR222 4.7 24.2 1.0
CA A:ALA182 4.7 19.5 1.0
OD2 A:ASP220 4.7 21.4 1.0
O A:HOH2025 4.8 20.9 1.0
O A:HOH2026 4.8 22.7 1.0
OH A:TYR184 4.8 21.8 1.0
CA A:VAL223 5.0 23.4 1.0
CD1 A:PHE50 5.0 23.4 1.0
CB A:VAL223 5.0 23.6 1.0

Magnesium binding site 2 out of 6 in 5a94

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Magnesium binding site 2 out of 6 in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:25.9
occ:1.00
 O B:HOH2134 2.1 21.3 1.0
O B:HOH2138 2.3 22.0 1.0
O B:VAL181 2.3 20.1 1.0
O B:VAL178 2.4 23.8 1.0
O B:HOH2133 2.5 24.3 1.0
C B:VAL178 3.4 23.8 1.0
C B:VAL181 3.5 18.9 1.0
CG1 B:VAL223 4.0 23.6 1.0
CB B:VAL181 4.1 20.4 1.0
N B:VAL178 4.1 24.2 1.0
CA B:VAL181 4.2 20.1 1.0
O B:TYR175 4.3 20.5 1.0
CA B:VAL178 4.3 23.7 1.0
N B:VAL181 4.3 20.4 1.0
N B:PRO179 4.4 24.3 1.0
OG1 B:THR222 4.4 27.3 1.0
CA B:PRO179 4.4 24.1 1.0
CE1 B:PHE50 4.5 24.1 1.0
N B:ALA182 4.5 18.6 1.0
OD2 B:ASP220 4.5 22.6 1.0
CB B:VAL178 4.6 23.2 1.0
C B:PRO179 4.6 23.3 1.0
O B:PRO179 4.6 23.9 1.0
O B:HOH2021 4.6 24.8 1.0
CG1 B:VAL181 4.7 20.4 1.0
CA B:ALA182 4.7 18.3 1.0
CA B:VAL223 4.8 22.4 1.0
CB B:VAL223 4.8 22.8 1.0
OH B:TYR184 4.8 20.4 1.0
CD1 B:PHE50 4.9 24.4 1.0
O B:THR222 4.9 26.2 1.0
O B:HOH2020 4.9 18.8 1.0

Magnesium binding site 3 out of 6 in 5a94

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Magnesium binding site 3 out of 6 in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:26.2
occ:1.00
 O C:VAL178 2.2 19.0 1.0
O C:HOH2134 2.2 22.9 1.0
O C:VAL181 2.3 19.7 1.0
O C:HOH2140 2.4 27.0 1.0
O C:HOH2137 2.5 24.2 1.0
C C:VAL178 3.3 20.4 1.0
C C:VAL181 3.5 19.4 1.0
CB C:VAL181 4.0 19.9 1.0
N C:VAL178 4.0 21.7 1.0
CA C:VAL178 4.1 20.5 1.0
CA C:VAL181 4.1 19.8 1.0
O C:TYR175 4.1 18.6 1.0
N C:VAL181 4.2 20.6 1.0
CG1 C:VAL223 4.2 25.9 1.0
N C:PRO179 4.3 20.5 1.0
CA C:PRO179 4.3 21.0 1.0
CB C:VAL178 4.4 20.6 1.0
C C:PRO179 4.5 20.7 1.0
CE1 C:PHE50 4.5 23.9 1.0
N C:ALA182 4.5 18.9 1.0
OD2 C:ASP220 4.6 22.4 1.0
OG1 C:THR222 4.6 23.9 1.0
O C:PRO179 4.6 21.2 1.0
CG1 C:VAL181 4.6 20.9 1.0
O C:HOH2029 4.7 24.9 1.0
CA C:ALA182 4.8 18.6 1.0
OH C:TYR184 4.8 20.1 1.0
CD1 C:PHE50 4.9 23.1 1.0
O C:HOH2028 5.0 27.1 1.0

Magnesium binding site 4 out of 6 in 5a94

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Magnesium binding site 4 out of 6 in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:26.8
occ:1.00
 O D:HOH2104 2.1 30.0 1.0
O D:VAL178 2.2 29.0 1.0
O D:VAL181 2.3 26.1 1.0
O D:HOH2101 2.4 30.8 1.0
O D:HOH2100 2.7 20.4 1.0
C D:VAL178 3.3 30.2 1.0
C D:VAL181 3.4 25.6 1.0
CB D:VAL181 4.1 25.8 1.0
N D:VAL178 4.1 29.4 1.0
CA D:VAL181 4.1 25.6 1.0
CA D:VAL178 4.1 30.5 1.0
N D:VAL181 4.2 26.2 1.0
N D:PRO179 4.2 32.0 1.0
CA D:PRO179 4.2 30.8 1.0
CG1 D:VAL223 4.3 27.8 1.0
C D:PRO179 4.4 29.8 1.0
O D:TYR175 4.4 24.7 1.0
CE1 D:PHE50 4.4 33.4 1.0
N D:ALA182 4.4 25.1 1.0
O D:HOH2017 4.4 22.7 1.0
O D:PRO179 4.4 29.0 1.0
CB D:VAL178 4.5 30.4 1.0
OG1 D:THR222 4.5 31.5 1.0
O D:HOH2016 4.6 32.3 1.0
CA D:ALA182 4.6 24.8 1.0
CG1 D:VAL181 4.7 25.8 1.0
OD2 D:ASP220 4.7 32.2 1.0
CD1 D:PHE50 4.8 33.1 1.0
CA D:VAL223 4.9 27.6 1.0

Magnesium binding site 5 out of 6 in 5a94

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Magnesium binding site 5 out of 6 in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg402

b:22.0
occ:1.00
 O E:HOH2149 2.1 20.9 1.0
O E:VAL178 2.3 17.8 1.0
O E:VAL181 2.3 18.3 1.0
O E:HOH2158 2.3 19.4 1.0
O E:HOH2152 2.5 22.6 1.0
C E:VAL178 3.4 19.5 1.0
C E:VAL181 3.5 16.9 1.0
CB E:VAL181 4.0 17.4 1.0
N E:VAL178 4.0 20.1 1.0
CG1 E:VAL223 4.0 23.9 1.0
CA E:VAL181 4.1 17.6 1.0
O E:TYR175 4.2 17.1 1.0
CA E:VAL178 4.2 19.2 1.0
N E:VAL181 4.2 17.9 1.0
N E:PRO179 4.4 18.4 1.0
CB E:VAL178 4.5 19.2 1.0
CA E:PRO179 4.5 18.8 1.0
OG1 E:THR222 4.5 22.9 1.0
OD2 E:ASP220 4.5 21.2 1.0
N E:ALA182 4.5 16.7 1.0
CE1 E:PHE50 4.6 20.9 1.0
CG1 E:VAL181 4.6 16.9 1.0
C E:PRO179 4.6 18.0 1.0
O E:PRO179 4.7 17.7 1.0
OH E:TYR184 4.7 15.9 1.0
CA E:ALA182 4.8 16.2 1.0
CA E:VAL223 4.9 21.6 1.0
CB E:VAL223 4.9 23.2 1.0
O E:HOH2033 4.9 18.0 1.0
O E:HOH2031 5.0 17.7 1.0
CD1 E:PHE50 5.0 20.9 1.0

Magnesium binding site 6 out of 6 in 5a94

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Magnesium binding site 6 out of 6 in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg402

b:27.0
occ:1.00
 O F:VAL181 2.2 21.2 1.0
O F:VAL178 2.3 22.2 1.0
O F:HOH2113 2.4 31.5 1.0
O F:HOH2111 2.4 20.0 1.0
O F:HOH2115 2.5 26.6 1.0
C F:VAL181 3.3 20.7 1.0
C F:VAL178 3.4 22.6 1.0
CB F:VAL181 3.9 21.4 1.0
CA F:VAL181 4.0 21.3 1.0
N F:VAL178 4.1 23.5 1.0
N F:VAL181 4.2 21.9 1.0
CG1 F:VAL223 4.2 27.1 1.0
CA F:VAL178 4.2 22.7 1.0
O F:TYR175 4.3 23.6 1.0
N F:PRO179 4.3 22.7 1.0
CA F:PRO179 4.4 22.2 1.0
N F:ALA182 4.4 20.6 1.0
CB F:VAL178 4.5 22.3 1.0
C F:PRO179 4.5 21.8 1.0
O F:PRO179 4.5 21.7 1.0
CE1 F:PHE50 4.6 25.9 1.0
OG1 F:THR222 4.6 30.5 1.0
CG1 F:VAL181 4.6 22.4 1.0
CA F:ALA182 4.6 20.4 1.0
OD2 F:ASP220 4.7 25.2 1.0
O F:HOH2024 4.8 23.1 1.0
CA F:VAL223 4.8 25.9 1.0
OH F:TYR184 4.9 23.0 1.0
CB F:VAL223 4.9 26.3 1.0
CD1 F:PHE50 5.0 25.3 1.0

Reference:

M.Lafond, G.Sulzenbacher, T.Freyd, B.Henrissat, J.G.Berrin, M.L.Garron. The Quaternary Structure of A Glycoside Hydrolase Dictates Specificity Towards Beta-Glucans J.Biol.Chem. V. 291 7183 2016.
ISSN: ISSN 0021-9258
PubMed: 26755730
DOI: 10.1074/JBC.M115.695999
Page generated: Sun Sep 29 00:21:18 2024

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